Trees | Indices | Help |
---|
|
Nexus class. Parse the contents of a nexus file. Based upon 'NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
|
|||
NexusError | |||
CharBuffer Helps reading NEXUS-words and characters from a buffer. |
|||
StepMatrix Calculate a stepmatrix for weighted parsimony. |
|||
Commandline Represent a commandline as command and options. |
|||
Block Represent a NEXUS block with block name and list of commandlines . |
|||
Nexus |
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|
|||
C = False
|
|||
INTERLEAVE = 70
|
|||
SPECIAL_COMMANDS =
|
|||
KNOWN_NEXUS_BLOCKS =
|
|||
PUNCTUATION =
|
|||
MRBAYESSAFE =
|
|||
WHITESPACE =
|
|||
SPECIALCOMMENTS =
|
|||
CHARSET =
|
|||
TAXSET =
|
|||
CODONPOSITIONS =
|
|||
DEFAULTNEXUS =
|
|
Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for mrbayes. |
Combine matrices in [(name,nexus-instance),...] and return new nexus instance. combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix. |
Delete []-delimited comments out of a file and break into lines separated by ';'. stripped_text=_kill_comments_and_break_lines(text): Nested and multiline comments are allowed. [ and ] symbols within single or double quotes are ignored, newline ends a quote, all symbols with quotes are treated the same (thus not quoting inside comments like [this character ']' ends a comment]) Special [&...] and [\...] comments remain untouched, if not inside standard comment. Quotes inside special [& and [\ are treated as normal characters, but no nesting inside these special comments allowed (like [& [\ ]]). ';' ist deleted from end of line. NOTE: this function is very slow for large files, and obsolete when using C extension cnexus |
Adjust linebreaks to match ';', strip leading/trailing whitespace list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so that no linebreaks occur within a commandline (except matrix command line) |
|
SPECIAL_COMMANDS
|
KNOWN_NEXUS_BLOCKS
|
MRBAYESSAFE
|
DEFAULTNEXUS
|
Trees | Indices | Help |
---|
Generated by Epydoc 3.0.1 on Mon Sep 15 09:22:36 2008 | http://epydoc.sourceforge.net |